Resolving Difficult Phylogenetic Questions Why More Sequences Are Not Enough 英文参考文献.docVIP

Perspective ResolvingDifficultPhylogeneticQuestions:WhyMore SequencesAreNotEnough Herve′ Philippe1*,HennerBrinkmann1,DennisV.Lavrov2,D.TimothyJ.Littlewood3,MichaelManuel4, GertWo¨rheide5,6,DenisBaurain7 1De′partementdeBiochimie,CentreRobert-Cedergren,Universite′ deMontre′al,Montre′al,Que′bec,Canada,2DepartmentofEcology,Evolution,andOrganismalBiology, IowaStateUniversity,Ames,Iowa,UnitedStatesofAmerica,3DepartmentofZoology,TheNaturalHistoryMuseum,London,UnitedKingdom,4Universite′ Paris6,UMR 7138Syste′matique,Adaptation, Evolution UPMCCNRSIRDMHNH, Paris,France, 5Department ofEarthandEnvironmentalSciences,Ludwig-Maximilians-Universita¨t Mu¨nchen, Mu¨nchen, Germany, 6GeoBio-Center, Ludwig-Maximilians-Universita¨t Mu¨nchen, Mu¨nchen, Germany, 7Unit of Animal Genomics, GIGA-R and Faculty of VeterinaryMedicine,UniversityofLie`ge,Lie`ge,Belgium In the quest to reconstruct the Tree of Life, researchers have increasingly turned tophylogenomics,theinference ofphylo- genetic relationships using genome-scale data(Box1).Mesmerizedbythesustained increase in sequencing throughput, many phylogeneticistsentertainedthehopethat the incongruence frequently observed in studies using single or a few genes [1] wouldcometoanendwiththegeneration oflargemultigenedatasets.Yet,assooften happens, reality has turned out to be far more complex,as threerecent large-scale analyses, one published in PLoS Biology [2–4],makeclear.Thestudies,whichdeal with the early diversification of animals, deepdivergences toberesolvedevenwhen usingverylonggenesequences[7]—butthis issue is outside the scope of the present contribution.Dependingontheaccuracyof the model of sequence evolution, multiple substitutionscangoundetectedorbewrongly inferred.Inbothsituationsspuriousphyloge- netic signals are generated; these constitute themajorpartofwhatwecollectivelyterm non-phylogenetic signal. The best known example of the misleading effect of non- phylogenetic signal is the long branch attraction (LBA) ar